Commit b39ff327 authored by Peter van 't Hof's avatar Peter van 't Hof

Added unit testing in toucan

parent 80dd2f50
......@@ -127,7 +127,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
annotation.foreach { toucan =>
toucan.outputDir = new File(outputDir, "annotation")
toucan.inputVCF = vc.finalFile
toucan.inputVcf = vc.finalFile
add(toucan)
}
})
......
......@@ -43,5 +43,17 @@
<artifactId>BiopetToolsExtensions</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_2.10</artifactId>
<version>2.2.1</version>
<scope>test</scope>
</dependency>
</dependencies>
</project>
......@@ -39,20 +39,22 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
def this() = this(null)
@Input(doc = "Input VCF file", shortName = "Input", required = true)
var inputVCF: File = _
var inputVcf: File = _
@Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
var inputGvcf: Option[File] = None
lazy val gonlVcfFile: Option[File] = config("gonl_vcf")
lazy val exacVcfFile: Option[File] = config("exac_vcf")
lazy val doVarda: Boolean = config("use_varda", default = false)
var sampleIds: List[String] = Nil
def init(): Unit = {
inputFiles :+= new InputFile(inputVCF)
require(inputVcf != null, "No Input vcf given")
inputFiles :+= new InputFile(inputVcf)
sampleIds = root match {
case m: MultiSampleQScript => m.samples.keys.toList
case null => VcfUtils.getSampleIds(inputVCF)
case null => VcfUtils.getSampleIds(inputVcf)
case s: SampleLibraryTag => s.sampleId.toList
case _ => throw new IllegalArgumentException("You don't have any samples")
}
......@@ -63,13 +65,12 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
)
def biopetScript(): Unit = {
val doVarda: Boolean = config("use_varda", default = false)
val useVcf: File = if (doVarda) {
inputGvcf match {
case Some(s) => varda(inputVCF, s)
case Some(s) => varda(inputVcf, s)
case _ => throw new IllegalArgumentException("You have not specified a GVCF file")
}
} else inputVCF
} else inputVcf
val outputVcfFiles = BedRecordList.fromReference(referenceFasta())
.scatter(config("bin_size", default = 50000000))
......@@ -127,10 +128,10 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val cv = new CatVariants(this)
cv.inputFiles = outputVcfFiles.toList
cv.outputFile = (gonlVcfFile, exacVcfFile) match {
case (Some(_), Some(_)) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
case _ => swapExt(outputDir, inputVCF, ".vcf.gz", ".vep.normalized.vcf.gz")
case (Some(_), Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.exac.vcf.gz")
case (Some(_), _) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.gonl.vcf.gz")
case (_, Some(_)) => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.exac.vcf.gz")
case _ => swapExt(outputDir, inputVcf, ".vcf.gz", ".vep.normalized.vcf.gz")
}
add(cv)
......@@ -139,7 +140,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
/**
* Performs the varda import and activate for one sample
* @param sampleID the sampleID to be used
*
* @param sampleID the sampleID to be used
* @param inputVcf the input VCF
* @param gVCF the gVCF for coverage
* @param annotation: ManweDownloadAnnotateVcf object of annotated vcf
......@@ -171,8 +173,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
add(bgzippedBed)
val singleVcf = new BcftoolsView(this)
singleVcf.input = inputVCF
singleVcf.output = swapExt(outputDir, inputVCF, ".vcf.gz", s""".$sampleID.vcf.gz""")
singleVcf.input = inputVcf
singleVcf.output = swapExt(outputDir, inputVcf, ".vcf.gz", s""".$sampleID.vcf.gz""")
singleVcf.samples = List(sampleID)
singleVcf.minAC = Some(1)
singleVcf.isIntermediate = true
......@@ -208,7 +210,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
/**
* Perform varda analysis
* @param vcf input vcf
*
* @param vcf input vcf
* @param gVcf The gVCF to be used for coverage calculations
* @return return vcf
*/
......
@HD VN:1.4 SO:unsorted
@SQ SN:chrQ LN:16571 M5:94445ec460a68206ae9781f71697d3db UR:file:/home/ahbbollen/fake_chrQ.fa
>chrQ
TCGGCATCTAGAAACTCCAAGTCTGCAGATCTATAACACACGAGGGTATTCAGCCCTAAAGCATTGCGTCTAGGCATGGGTCTTTAATCTCGCCCCGGCAACCTCTACGCGAGCTCCTACCAGTCAACGTGATTGATCCCTCGTACCTAGCATATTCCACGGCGTTTCATAGCCTTGACGGGCACCTTATCCATTTTTACCTAGTTTGACATTAATTGCTTCAAGACTACTGCGGTACGGGTCCCTGCATCCAGAAAGGATGACAAAAAGTGTGACAGTGCGTTCAATCCATAGATTCCCGTCGGTGCGAGGGCTGAAGTTGAGCCCTACAACCCGGCGATAAAAATTGTAACCCTATGCATTGCGTCAAGTTAAGACCCTCCATCTTCGCCACGCGATAGGAATTTGAAACATCGGCGTGCTTAGAAAGGCTATTAGCGCGGGTGGCCTGATCGGTATCCGATAAAGGCGTTGCCACAAATTTTGCCGATTGACCTGCAATTACATCGGGTAAGTGCATTTCCGCCGTTAGAGTATTAAGTCATGACGTTTTCGACATGGGCATTTAATTGGCCCAAGGTGGAATATTCCTGATGTGCCTAAGTATGAGCTCCCCATGAGAATTTGAAGATCATGAAGACTTGAGTCAATTCTAAATGTAGTTACCATCACTTAAGTTCGTTCGCCTTCTGGGCAGGCTATGTCTAACGAGCGACGTCCGCAGTGTGACAATCTAGATATTGGTTGAGCAGGAATACCAAGGAGGTGCTTGAAGTTTCTCTTATGGAACCAACTTCAATCAATAGGTAGTCTCCGTTTCGTTTCCACTGAGACATTTGTGCAGTGGCACAGTATGTGGTCGTAAGCGCATGGTGTTGTTGGAACGAAGACTCTCACTTTTGTTTCCTTTGGTAGTTTAATTTAGCAGTATCCTGGTCGTTGACCAATTTGTGAATCTCCACGGTCTCTCTTTATCAGTCATACCTCTTAAACCGGCTTCCGCTCCTGCGCACATTTATATCCTACTTTCCGTCAATGTGAAAGAGAGATCAACATAATTTCGCGCACGATCTGTCCCATTTCAGACGCCATCGACGGGTCCCGCCTTCACAAAAAACCTGCCACCATGCAGTAGGTACCTCCATATGCTGAGCGTCCGTTACCGGAAGGGTTAAGTCACTGTTTAAAGGATAAGGCGAGGTTTCCCTTGGTGGTGTACTACTGCTCACGTTCCTGCTTTACTCTCCGAGTATTGTTTTAAAAGTGGGCACGCTGGAACGCAGCACCCTATAAGAAGACTCAGTTAGGTCCCCTTCACGAGCATGTTTGAGCTCTCGGACCTAAGACGTCCGAACTCGGTTACGACGGTTAAAGACAAAGCTCCCAGCATGGTATCAGAAGCCACCACGCGTGAGGATGGCGGGGCCCTGGGCACATTGGCCCCGAATTCTTCGCCCACTTAAGTCGGACTCACCACGGGAGACTACGCCCTAACCGGATAATATCTTTTAGATACCATACAGGGTGCAACCATCGCGGCGTCAGCTGAATGTGAGGACAGAGCCCCACACACAGCACTAACAGATCCATGATTTTACTTCGTTTGGGCGACGTGCGAGCCTATTCGGCCTGTCGGACTTTGTGTAGATTCGGGATTTGACCTAGCGTATAGGCCTTTGGTATACTCGAATTATCAGGGTCAAACTACCCTCAAGGAATCCTATTTCAGACGGACGTTTGCCACCCCGGAACGTTGTCGGATCGCTTCTTGCCGCAGGAGATTCATGGAGTGATAATCGCTGGACTCACAAGTGTCAGCGGACTTTCGGTGTCTTGTGGCCTACTTGCAGTGAACACCACCAAACGAGTAGTATTATGGATTGCCGGCGTGTGTTTGTGGCCATGATTGGTTGATGCGACGGCCTAGATTCTCCTACGGGAATCTACCAGGCCCAAAAGCGCTGACTTTTATGTATTTGAGGGGCCGAAATTACATAGTAACCCAGAACAAATACCCGTTAGTTATAAAGTGAGCGCATAAGTTTGGTCGATCCGGCAGTCGAACCATTGCGGTCGGACATATCCGCAGTAGTACACTAAGGCGGAATAGACTGCCGAGTCAACGCTCCCTCATTCTTGCTACCTTAGATCTCGCAGGTTCGACCATTGCTGAAGCCGCTGAATTACACGAGTTGTTTTGTTAACCCCCGGAATGTAGTTCGTACGCCTCAACTGATTCTTCAAAAGCTCACTGCACGTGACTTGTCATGTGTTCCTAAAACATACCTCATCTGTGGGTCTGGTCCCATAAGCATGGAATGTCCGTCGACGCAACATGGAAACCCACTCGCTCGCTATACGTTTATGGTGAGACAGAAACACACTGTATTAGACTGCCACTGATAGCCCCAGTAGCAAGGTGATGTGGCAGGCATGGTACCCAAACGTCTATCGTTTTGGGAACCAAGGGGAGTGCTAATAGGTCCGGCCACGTAGAATGACATAACCTCCAGAGGAGCGCAGGAGTTGATGCATTAAAAGATCCATACTAAACGTTAGCTTAATGCCTTCAAGGCACCAGCTACCTCCATGACAAGGAGATTTCGGAAGGGGTAAGATTTACTTCTGTCCCAAAAGGGTAATGACCCGTAGGGATGGAATCATTGATGAACTCTAAAGGGACTCAGCCGACTAGCCGAGAGGGCTGGACGATCATTTGATGGGAGAATACGCATACATCTAAGTGTCAAGTATTAAATCGGTAATCTCCGTAAAGGCGTGAAGTTCACAGGGCGCAGTTTCCAGTTACTCCAAGAAACTACCGGTTCAGTTATCGCTTCCGGTGCCTTCACAGCAAACATCATTCGCTCAAGAAAGTGCTGTCGCTGCGTGTGGATATTTCCCCCTCGTTCTGGAAAGTGCTCTCAGCGACGCACGTAAACATGCTGGCGACGAGAGAGGCGTCAACACGGTCCGTTACCAAACTGCGGCATTTACCACGAACCTGATTGCAAAGTGAGATTTCCGTAAGGAGGTTAGCCAAATATTACGTAGAGTGTTCCACACCAAATCCGTCGTCCACATTCGCGACGGCAGTCTAGACGTGTAATTCCCCGGATAATCCAGTTACTACATGCTGATGCAGTCATAGTGCACGCAAATGCGCAACTTAACAAGCACGACCTGAAACAGAGAACCCCTGTGTAGTCAATATAGGATGACGGACACACACACTTGCTGCTGCAATCTTACATTCTGCGAACGAGTGCAAAGTTGAAATCATGACGAACAGCCTTGCTTTTCAGAGTCTCTATCGAACTCCTTTACACCTCCATATCTACTTGCAAATCACACTAGAGGGGCGCAGCTTACTCACTGAGAGATGGTCTACCTAATCGATTTTCGGTGAACTTTGAGTACAGCATTGAGTCTGGAGGGTTCCACTACTTTATCGTACCGGTCCGACATGATTTCTTATCGAATAGATGTTGAGATGGACATTAATAAGCATAGTACGTCTCGATCGATGGCTACCTTTACGTCTATGAGTGCTTACATAAGGTCTCTCGTAAGTCATGGTCCCGCGGGGCTCGCGCAACATTGTGGATTAATGACTCCAGTGACGCATGTTCGATTCGCATGAAGTAGGTGGCGCGTATTCATACATGAATAGTAGGCAGAACGAGCACATTGGACCGATCTTGGAGGTTGGGCTTGAGGTCCCGCACTGATAGTTTACGGCCATGAAGACGACAATTGTCAATACTTCTCTATCCTGAGCGAATGCTGACGGGGGCCAGGCGGAAAAGTGCGACACAGTCTACTGATTACGTGTAGTACGTGGCTAAGCATATTCCCGGGTTCGCAAACATAGGTCTCTGATGGGGTATGGGTAAGAAATCTGAAGGTTGCGTCTCTCACCACGGTCAGGATACCGAATCAGCTCATAAGAGTTACAAACGCGCAAATGAAGGCCTAGTCCACAGGGGTGTCATTCGCACGAGCTGGGCTTAGAATCACTGTTTTCGGTCGCACCTGTAGGGGGACATGGGACGGATTTCACAACAAAAAAGCATCTCTCATGATTCGATTCAGATAGAGGAGAGGAGGTAAATGCCAACAAATCTATTCTTTAGTACCGCCTGACGGAACGTATTTAATCCTCGCCTCAGATCGACACCGCAGGGTAGCTGAAGACGTCCGTTCTTAGACATTTAGTCGATCATTTGTTATGAAACAGAACTAGGAGTCCGTGCCCTTCAGGCCGGCTCAGGGGCACCTACCTCCAGATCGCCCAGGTTGGGTTTATTAGGCGCCGAAAAGTTACTGCCCTATCAGCCCCTCCAATCCGACCTACGGACATCATCCCACTGGCTCGCAAAATATAAATTGCGGATGGGAAAGGATAAGGAAAATCATTACCTACACAGAAGGACAATGTCAGTTCCAAATAACACTGATACTTTCGGAGCAACTTGGTCCGGAAATGTAAGTACGACTATAGCCCTTTCGACCAACGCCGACAGTCCTATTTGGACGCCGAGAGAGGCGACGGGTAGCCGAATGTAAAGCTCTCGGGTCGCTCTTGGCGGAATGCGCTGCGGGTCCTACCCTAAACCCTTACCACCACCAACTTCGTTAGGAGCCGTATAGATTACAGCTCCCGCAAAATTAGAGAGGAATCTGAGTTATTAGCTGAGGACCCCGCATTTTCTGCGACGGCGTAGCTGCAGTGACGTACGATATGAGTTCCCGACTGTGAGGGAGTCCCAGTCGTGACTCCCTACAACGGCTCCAGATATTGTTACTTATGGTCAATATGCCCCGACCGCCCATTGTCTCGAGTACAGTCTTCCCCAAAGTTAAGCTGTGCATTACCTTACCGTTTTAGGTCCAGCTGGTAGCACCGAATGCTGCGCAATCCGAGCCCCCGAAATAGACTACGTGTCCACGGTCAATTGTCATGGGTAGCAGAGCTCAAAGAGGAGAAACGTGCCCCGTAAACCTATTAGATCTCGGTTGATAAATATCAGGCCACAGCAGGCTGCCCGATGCTTGTTTGAACAACAACTTCGGGAGCCGCGGTCCTTGGTTCTCCCGATATTCGGCCGCACCGAACGGTACGCGTCATCGCGAGGTGCGTTCTCGCAGCAAGAAATATTTGTTGTTGTTGTCTTCCTTCCGCATAGGAAACCTTAAGCGGTACCTTTCTACGAAGTTGAACCCTAGAAGCACGTGTAACAATTTTTTTTACGCTACACCCGGATCTGCTTCCATCTGTTGATCATATGAGCCTAATGTGACTAATCTGTGCCGTCGATTGAAAATTCGTTCTGAACCTAATCACATGAATTAAAATTAGGGCGAGAATTGGCTCCTTTTGGGCCGTAATCCTTCAAAGGGTTAACCGAATTTAGCCTCCACGGTGACACAAACTCCCATAGGTAAGGCAAACCCAATAACGAGGAAGCCTTGCCCACAGCATGTTTGATAAATACCCTTAGGGTAATATCGCGTGCAATACTGAAGCCGCTCTTCTAGCATCCGTGTTTGACATACTATGACCTTGAAGCCTGCCGCAGCTTCTAGGTCATCCAAGTAGATCAAAACGCCATGTTGTGGATCCATGCATCTTCCCAGTGAACATGGATCTTAGTGTGACAGGCGAGGAGCGGCGAACACTATCGGTGTGGCAAGCTCGGGCCTTCGTACGTTGTGGAAGTATGCGAATAAGGAGACCGTAATGTATCAAGTTCTTAAGAGCCTTGGTACCGTTGCAATTCGGCATGTTCCTACAGAGACACTCCGTGTTTGTCATCCGTCATAGATCTATGGCGTAGTTAGCGCCTCTGAAGTAGTTGTCCATTCAGCAGGCATTGCTTAGGGAGTTTCTGGCGCTTGCCGCTCAAGATGCTCACGGGCCTAAGTAGCACGGCAACCTTTTGACAAAGCATTTTATAAACTGAGCATATTGGCCCGAAACTAATCCAGCAAAGGGTGAAGACCTGTCAGCGGGCCCAGAGTGTGAACGGTCTACTGCGCGGTACATAAGTGGCGTAATCCATCAACAAGACCTACACGACCTGAATGATTTCCAACAACTTTATATGCTTTTCCGCATCTCGAGAGTACCGGAATCTATGCAATCTCCCAAGGATCCGTAGATTTGAAATTCAATCCGACGGGGTAAGGTTGCCGCGCCGGTTAGCTAATGTGCGGATTTATAGTCTTTTTCCCAGAAGGCGTAGTTAGTTTCGCACCTAACTACGACACATACTTGGGTCGACTGTTGAAGGTGGTAAGTTGCGAGCAGTCCGCCGCTCTCACGCGCCGAACCACGTTCATATCGGCAAAGTTGCGCGATGACCTATAGGTGTGCAAAGCTCGTCCGACATTGGGATTGGATTCACGTACATACGTTAGTATCATGGGTAAGCTTCCATGTCAGCCTCGTGTATAGCACCGGTGCGCCGCGCGTTAAGGATTCTATGCCCAGCAAATGTGCCAACGTTGTGGGGAGAAAAGTGTAGTTGGATGCGATCGTGACATCGGCACACCGAAACTCTGCAGCCAGTCCCGCTAATCTCATTGGCACCGGGTAAGAGATTACCTTTGGTTAGGAATCGCGTGCGACGTACTGCACGAAAACAGTGCCTGAACCGAGGTGTTTACTTAGATGGTTCTAGACCCAGCATGTTCCTCACTGGAACCTGACGTCGGTACGTGATCCTCTATACCTCCTTTTCGGTATTGGCCTGGCAGCTACTCTAACTGTTTGGGCCGCGCCGATTTCTCGAGTCCACACGGCGAGGTCAGCAAAATTGCCAGTTAGTGGATGTTGGGATCTCAACGCATTACCATGAGAGTTCTTGGTTTACCCGTTAACATCGCTGCGCACGGTGTGAAAAGCCTGTTTCTTTGGCCCCCATCATCTTCGGCCCGCAGATCTCAGATCAATGATGTAAGGTTGCGGCGGCAAAGACTAGACTTGAGTCGTGAGATGGTGCTTTGCTGAGGCCGTCTCCTATAGCTTATTCTAGGACTTTCCGCAAACCACCCGACGTGCGGCTGTCCACGATCGGATTCCATTCTGTCTCGGAGCATACAGCACTAGATTTGCCGCTTGAAAAATGTTCCATAACCATGATTTCAACCCCATCTAGTCGGCAGGCACAGCTGAGAACAGCGAAGGGCGTCGTGAAGGGCATTGCCCGTAGTGTTTCAGACGTGCTAGAGACTAAATCAACTATCTGCACTCGTAGCCTGGCGTGTGAGATGTCACCACGATGTGCCTAGAGGAGTGATTATGAACATGTATTACCACGTCCGGGTGTCGACGGCTATATGGCTAACATTTCTTATGGCTAGACGTGCTTGGAAAGGTTCCCCAGCCTTCTGTTTCCCGGTGCTTTCCACGAGTCTGGAGTTCTGGTAATTAACTACATGGCGTTAACGCGGAGGTAACCCCCAGTCATTGCATTGCAGGTAGGGCTTAGGTGCAATATAATTCACCAAGGCGCGGATTCCTCACGATTGTTACGAAGACACCCGGAGGGTTTCAGTATGGCTTGAGAAGTGTACGTTTTTCCGGCCAGGGTGTAACTATAACCAACACATGTTTGGCCACGGGCTAAGTCGGTCCGCACGACTGATTTCCCCCGCCCATGTGTTTGGGAGCAATAAACTGCGTCTGCCAAGAGTAACAACTCGAGTAGAGAAGGGAAGTCTCAGACTATTTTGCAAATCAGACTGTAAGGCTCAACAGCCATACAGCTTGCCCTACTACTGAATACTAGCGTAGCGTGGCCACATAGGAAAGACTTCATGTCTTCTAATAACCTTTTACCTCCAACGTCCCCGCCGTCTTCACGCGGTCCAACGATGAGGAAACAACCACCCCTATCTTCCGCGGAGTGGTTCACACGACCCCCGGCGTTAACGCGCACGTTGTTGTCTTTCGGGACGGCACTACCCCCAAATGCCCAGACCCAGTGCTAGCGATATTCAAACGCCGTCCGGTAAGTCCTGACGTTTTTCAACTGGATGCACTGGCGACACGTAGTTCGCAAGGCGTCCATGAGAGGTTTTAACCGTCATGTTTCCGTATCACGTCTTATGTCTGTCTCTATTCTCAGCGAAATTCTCATCATAGGGCGGAGACTATCTGAAGGCCAGCGAATACAAGATTTAATATCAAATATAGCATGGGGGCCAACAGAGGCCCCCCTGGTGCTGACGAATTATCGTGATATTAGTACAGCTGTCTGCAATGCCATTTCGAAGGCTTTTTGTTCGTATCACTGCTCTATGCATAGCGGTCACTATGACCTCTCAGCTTGACTCACCCGAATGACCAATTGTGGTCCAGCACTCCCTCATCTTCCCCCATTAACGATACGTTGGGCACCATCGGTGTGAGCTACCCGTTACAGTCATAGAATCGTTCTTTGCGTTGTACGCGGCACGGAGGTGACCGGGAAAAGCGCCGCGAAGGCCCCGCACTGAATAAAGCTAGTATTAGCGTCTGTCAAAGTGTTTTGACACCTAATTCGCTTCCAAGTCCCAATATCTAATCTAGCCTGCTTTGGGCCAACATCTCATTGCGTTATGCTAATGAAGAGGGTGCGGGATCACATCCGCTCTTCTCTTCCTATACACAGCGGACATTCGGGTTGGACGTTTGGAGTGATAATTTATCGTTAGGGATAAGTATGTCGGCGCTTAGTAGTATAGCCCGCTGACCAGCGTTCGATTTCGAACCTTACTGGACATTCTCAATAACTACTGATCATGACGTTTTCCTCAGTTCCTAGCCTTGACAACTAGCCACAGTCAGCATGGTAGAGAGCGTTGAGCCGGGGATAGCCAGGCTATTAAGACAAAGACCCTCGGGCCCCTTAATGCGCGTCAAGTCTGACGGTTTGAGTGCGGAGCAGTAAGCGCTTTGGTATAACCGTGACGTAGCAGATCCATGCTTCGCCCGCTTCCACCTGAGAGATACTAGCCTCTTTCGCACTTTGTAGGATTACGGGCAGCGAAATATTTATCCTGTGCGGCGAGCCCGCTTCGGTTTCGAGCTCTATCAGTGCGCGGTTGGCACTCCAACGCACGATAACATATACCCGCCCACAAGGCCATGCAGGTTTAACCTCCTATTCTGATTGTACCTGGCTGACTTTACGGTACCCACCAGCGCAGGATTAATAGCCTAATTATGCTAACCGGTGCTAGTCTAACTGCTGTTACTAGTCCGCCCCAGCTACCCCACGGGTCAGTAACTGCACCAGCAAGCATGGTTCTCCTCCTGAAGTTGTACGTTCGAGAACCCCGTATCGAGTTGGTATATAAATTAAGGGTTGTCTAAAACAGAAGCCTATTCCGCTATCATCGGTGTAATAACTGATCGCGCCGTGGTTAAATGGAGGAGCACCCGCATGGATACATCGCTAGCGTCTTGTAACTCTCTGGGGGCCTAGTATGGAACGGAACAATGACATCATTGCTTACGGGGCCCGCACTTAGCTGTCGCGTATCGCAAATCATATGGCATGTCAGTCCCGACATCACGAAAATGACCCCATCTGAGGTGGTCGGGAGGCGAACAGTCGAATATGATGTATGCACCCGCAACTTAATGTTCAAAGGCGGGCGAAATGCCTTCTCCCGTCCGGACTATCCTGAGTGCTAGCCGCGAGTCTGTAAAGGTTGACGCAACCATATAGCACGCAGAAAAATCACTCTCACACCATGAGAACCATGGCGGCACGCTGTCTACTTTGTCTGACAGGCTACGGAAGGAATGGTACATACGTACAAACGGATGATATGATATCGGTCATTGCCTATTGTGACGCTACCCTACTGCATCACCCCCTTAGAATGCGTTGGACGCTCTATAGCAGATCCTCCATCCAGTGGAAGTCTCGTCGCCGTGGTTTGCCTTAACGACCGTTGGAGAGAGCAGGACAGAAATATCGCCCTTTTGAGCGCATTATTTGGAATCGAGGTAAGTCAGTGCGGCATAATCGCGCCTCGTGAGCGGAACAGTTTTTGATCCCACCCGCTAAATGCCAAGGTGCTGTAACCTGGGCGCGACACCAAAAGACCACGTGCTGTATGAAGCATGTGTTCTAGCGCACTCTCAACCGTTACCCCGAGAGTAAAATGTTAGTTGTAGGCCGATTCTGCAATGGTAATTGGCGGAGTGTCTAGGGAAATGTTTCGGTCATACTTAACCGGCTACCTCTTCCTCCCTCAGATTCGGTCTGAGATGAGATATACTGGGTGAGTTGAGTCGCCCTGTATCGTTGCGGCGCTCGTGGACCAGACAGACAGTTCCCGTTTATCTCTGCTTCTAGATGGAGGGTCGCCTCCGTGTTAACGCCGGCGAAGGTAGTCGCAGCTGAAGTTGTGATGCACAATCAGGTGAGCCTTTTAAGTATGGTCCTACGGACGTGAACAGCTGGGCCCAGTCATTTAGTACGGGGGGTTTACCTATAAGGATACGGTAAGAACGTCATCTATCCGTCCCACTGGAGTCCGAGGGGTTCGTGTCTACACGGATTACTTATCATGCACACACGTCTACGGTCATGCATAAAGTTGTGCAGCGCAGCAATCGGAGCGGAGTTACACCATCTCCCTATTAACAAGGCACTTATTAGTACTTACCCCGTTATAGAGCTCTCATCTTATCGATAGAGCGCAGTCCTAAGTATTGGCTCGAGTGATTCGCTCCTCAGCCCTTGATTGTAACTCCCCCGATTGCAGGTTGTATGGTGAGTAAAATCTCTGCGCCCTTCTGTTCGGATAAAGAACCCCGACCACTAATGCCCGCCTGCTTGTTGGGCGGTAAATGGGTAACGGAACATGGACTATGAGTGCGATGATGGTCAATAGAATTACCTTATTACGCAGTAAAAGGAATGACGCAGACAGGTATTTGTCGACGATTGCTTCGAACCTGGCAAAATGGGGAGGTATCCTGTCATGTTCATCTGTAAAACAACTCCTGCCTCTTCGTAGAGGACACACACTGTGGGCCTTTAGCCTTTAGCAGCCCATTGGGGCTTACCAGCTGTCGTCATGGGGTATCATTAAGATCCATGCGCCCCCGAAACTTACTGCAAAACAATATGGCTTAAAGGTAAAGGGACCATCAGGAGAATGCTTAAGAGCGACATATAGATACGTATTTAATTAATTTATGTTAACGCAACCATCTCGCAGGAGTCGCATAGCATATTGCCGGGTGATAGTTAATGCACTGTGCTTCCGTGTTTATATAAAATAAGCAGTAACCTCTGACAGGTTGAGACTCCAACAAGTGCTCCGGGTATTTACCTTCTACCATGGCGTTCTAATATCACGAAAGAGAAATTGTGTGTACCGATGCCAGGTGACCGCCCGCGTGCGCCAACGACGCAATCTAGAGCATCCACGCTGAATTGGGGAACTCTTGCCGTTCGTCGCATGGTGTACTTGGTACCACTCGATATGCCTGATTAGGTTTGGCCGTAGCACGTAAGGTAGTGACTTTCCATTCAAGCTAGCGAAGCGACACCACCACAGTGCCCGGTCAAAATAACCCACACCTGGCCAGCATAGAGGCTAAAATAGCTACAGTGCGCTAATCGAGTGTTTTTGCATCGGCTCGTGGCTGGTGGACTCGGGACAGCTTAGAACTAACTCTGGTGTACAAACGCGATCGTAGCTCTCGCGACTTACTCACCGGAGTAGGTTAGATGGACAAGACCTAACCCGAAGCCTAAATCGCCCTGAGTGTTAGCCGCCATTCAATTCTATGGTTTATCGGGGGCGTCTATGGCTGCGACAGTATGGAGGCCCGTTATGGGCACCCGAGTATCGTACCATAGTAATCCCATATTCCTCTTCGAGCGACTATTGGATCAACATACCTACAGGGTAGTATGAATGTTCTTGATTACAGAAACCATGGAATCGGCGCATTCTATGTTTCACTTCCGAATAACAGTGAGCAAGGCATGCCCTTGACAAGGATCATCCCGACAGCAAGCCGATCGGGCCCTAGAGCCCGACCCCCAAACAGAACACCGGCCACGTAGTTGCTGGGACTAAACAAAGGTGTGTTTCCATAAAAGGAAATCTTCAAGTGTATTGTTGAGTCGTAACGCTTATATTTATGGCCCAATGGGCGTTGCGAGCACAGTAGCAGGCCTAGATGAATGCCTAGGCCACGATCGGGGGGAGGCTCATTGAACGTACTGCCATACCAAGCCCCCGTATGCTATGGCAGGAGGGGTTCTCTTCGTATAGAGCGAGGGTCTCTACGCCAAGCAGCATTCCCGTGTTGGGTGGCCAATGGGGCTCACTAGAAACTCGGTTTTTTTAGCGAAGGAATGAGCAAACTCGTGAAAGGTGGTACACACCAGTTGCGGCCGATTTGTTGTAGCAACAAGGTTTGAAGAATTGAGTAGATGGGCCAATTTACCTCCTATTTAGCGAGTGAGATGGCGCATGTTTATTCAGACTCCATGTGGGGTAGAGGCTAATCGTTTAGTAGCAATAACCCCGCGGGGCAAGAGACCGTAATAACTTGAATCTGTGGTAGCTATGAATATGTGCTTCGCCCTAAGTGTTATGTAACAAGAGTGATCCAGGGGCTCAGATCACACTTAGTACGATCCGCTACTGAAATGCGGCCGCGGGCTTGCACGCTGGACATAAGTCGGATAATCAATTGCCTACGACAGGTTCAGCCATAAGGCTTGGCTCCTAACACACTCATGATGTCTGGCTTTTACTCGTGCCCGGACATAAACGTATGCTCAAACGCGAGACAGGGGAGGGTCAGCACCGTTTAGATCTATAAGGCCTACCGGTAATATGGATCGACAACAAACAGATGCTATAGGGATACCTACTCCTTTGGACCCACATGTAGATGAAGGCAAACACGCAGAGCAAAGGAGAGTAGTCCACCCGGTATAAGTTTGTGCTTTGAATTCTGGCTACGCAGACTTGCACTCTGTCCCGGCATTCACTATACTTCTCCGGAAGTCCTTTAAGAAATGTCCGCGCTCATGTGGTTCCCGTTGCTCAGGGGCCAACTCAAGTAGATCTTTAAGGCGCAGTCGACCACAGGCTACTAGATACGAGTTATACTTATCCGGACATCTGGCTAAATACTTGGATACGATACTTCCCCAGTCGTGAGAACGAAGCTAATACAGATCGAATTTCGATGGTTCAGGCAGGCAGTTCTCAGGAGGCAAGGTGTTAAATAGTTTCGGAGGCTCTTTCGTACGATCAGGGTCTACTACCCTAGGGCATTTTGACTTTGGATTAAATATGCAAAATGCAAGGCCGATTGTGATCAGTACTGATACTCCAACTGGACCACCTTCAGACCCTTCGAGGGGACCTAGACGACGGGAACCCTTCCAGCGGGTGATACCAGTTAGAGCAAGTCACAAACACGATTCAGCCCCCGGGGTTTATGACGTACCATGCGAGTAATAATGCACGTATACGGAGCTCTTCCACCGAGCGATGGCATTTCGGGGCGAGGTAGTTGTCTTTCATTGGCATCGCACAACCCCCATCCTCTTAATTGGCATCGTCTCCAGCTGGAAAGAATTTGAGTGAGCATGTCGCCCCTATTATTCCGTTGCCAATAAAGTGTCTCAACTTTTGGCGAAGGTTTTAACGCATACAAGGAGAAGCCGCGAGACGTCTGTACCGCTGATCTGGACGCAAAGTGCTCGGACTGCCGCTGAGTTATCCTGGACGCCATGATTAGAGCCGTCGTCACTACCTGCATACATGGGCCGATAGAGTACTGCAACCAACAACTCACTTAAGCTCCACAACGGCTGGACACTTCCGAGAGCGGTCTTACACAAACGTTAGGTCCTGGGCCGCCGACCTTACCGCTAGTTAGTGAGAGCCAGTTAAAATTATGAACGCTCGGAACCTTCCCAACAGTGGCCGCAGCCTTCCTTGACGCCTAGCACATCTGGTTTATACTCGGGTATGCCGTAGATCGGTAACCTAGGGAACGACCCTGTGGGTTTAACACCCGAGTGCGTAATCAAGCCTAGAGGCCATCTCAACTCGAGAGGTCTCCTGACAAAGAGGCGCCCGATGAATCATCCAGAGGCGTCTGGCGGTCCTACGAGAGTGGCTTTGGATGCCTGCCCCTTGGATGGATCTGTCTTTAATCGGCGCCAATACCTAGCACTGCTAGGCTCCAGACTGTGTTTACATGCCGTAACCCTGATACTCGCAGAAACGTTGCTGGAAATTCCTAGCAGCTGAAACCATTCCCCGTAACGTACTAGTACGCTAAGAGAGAGTCTCTCCTGGCCCTGATGAGTGTGTTCTCATCTGGGGCACGATACAAGAATCGGAACGAACGCAATGCCGAAGTCCCTTGTACCTTAATTTGGGCGACGCAGATAGACCCAAAGATCGCGGACTACGGAAACTAGCATAGGACCTGTGTCGAGAAGGTTCGAGCAGGTAGTGACACGCAGCGCGGTGGCCGGCGGGGTGGCACATTGCGGGTCAATACTGGTAGTAGCCACTCTTTGGACATAGCGGCGGACCAGCGCCTAGAATGTCTCATTCTCATTTTGTTCCGTGGCACGTTACGTAATGACGGCCCGCCAGCACCTGTGTATGGACTTGTAGCTCGGGCCTCTGGTCCTGGCACGACAAGGCACCAGCCAGTAATCTCTCCTAAGGCGCTAGCGTGCATAGCGCGTCTGCCTACCGCCAGAGAACGCGTCATCTGCAAGACGTCCCAGCGTAGTGAATTGTAACTGCAAGCGTTCTCTTACGGTCATAGTGCCGATTTTGAGCAGTAATGGAAGCAGCAAAATGCCGCCCAAGCGATTCGCAAACTTCTAACAGAGCTACAGCCGGACACGACGCGGTGGTGCTCGCGGTTGGTGATCTTATGATATTAACGCCCATAGCGGCCATCTTAATCGACACCATGTTCGTTTTGGCAGGCCTTGTGGTAAACACGTGCTAGTGGCACCACCCATGCCCGTGCCCATACATCCAAACCGAGAGAAAGCCTATTTAAGCGAAAACCACAACTTCGAGGTTTCACCCCCTGCCATTGATAAAGCGAGGAGTACCCCCGATGCCGGGAAGCGTCCGCACCCATTTCTTTCGTTCTGGAATCCTCGGGCGACTTCTCGAAGATACTGTGCTCACGACCTGGAGTATCATGAACAATCGGAGGAAAATGAGTAATTGTCGAGTCGTTGTTAGACGGCACTTCCGTCCGGCCCAACTGTTCTCGGATACGTGTCCCGTGGTCAATGCTCTAAACCGGCTGCCGGCGACTCAGTTCACTGAGACAAATTCTGATGCTTTCGAAGCAAGGATGCGCCCAGAGCAGAGCTGCCCAGATGAGGTTAAGAACGTAACTATAATCGATCAGCCATTCGGCTTAAGGGGCCCCGGCGAAACGCGAAACACTTGGCACATGGACGCTTCACGCGCAACAGTAGTTGTCTCTTTCGTGAGCCACCGTAGCAGCTAGAAAGGCCTATCCAGTGATGCTTTATGACTGAGTGTCGAATCTAGGTATAGCATAGACTGGCTGATCGGGCGGGTCGGCCCACCCGTCTCGGTCGAGCGGTTCTGACTTTGGGTGGCTGTGTGAACCCAACTGCAGATGGAGTTGAATGGGTACACCCTATGCGAGGCCTCGTCTTTACACCAAATCGGGGCCCTGTGAAGTGCCACTCTTTTCCAGCCGGCAGCCGCTCAGTCTGATTTTGCTTGTACATGTCGTGTGCGAACGTTCCGGGAGGCTTCCGTGTTCCAAATACCGTGTTCTCATATTCGGTCCATCTACCGACGGAGAGTTGGGATGCCCGGGCCCGGAAATATAATTTAAACTCGTGGCCAAGAATTTAGCATGTTGTAAACATGAGAGACAGGGCCGGGCTAAAACATTACCCCTGAGTAATGTAGAGCCACAACTGAACATAACATTGGGATCTAACGCACGCAATCAGTGTAGCTTCAGCCCACCCTCTAAATTTCCCCCGGACAACTGGATTATCACCTGCGTCACGCGATAATTGCTCGCATCTCACCAACACACTTCGACAAATCTGGAGTCTCCCTGGTCCGTACGTCCAAAACCGTTTAAATGGGCGGGTGTGTCGTGAACCAATCTCCTCTTCCATTTGTCACATACTGGCGATGACATCCTTTTACTTGAATTATTCATCCGGGCACCAGCCGCTTTCCCTACGATCCCCGACACTCGGGGCTTCGGGAGTTGCCCGCCAAAAAACCGACAAACCAAACTATACAATCAATCCCATCTAGATGTAGGGGACTGAGGCTCTAAGCTATGCGCCTACTATACTTTGTAGGTATCAAACTACGCTTGAAGATAGTTGATAAGGAAGCGAATTGATCGAGTACCGTATCTTCAGTCCGACTCCCGTTCGAACGCAGCACGCTAACATGGTCCACTGGCATTCTTACTAAATACCTAGTTCACTTCTACATGAGGAGTGTCTGGGCCGGACTCACCTTTGATTAGATAACTGAAG
package nl.lumc.sasc.biopet.pipelines.toucan
import java.io.File
import java.nio.file.Paths
import com.google.common.io.Files
import nl.lumc.sasc.biopet.utils.config.Config
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by pjvan_thof on 4/11/16.
*/
class ToucanTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Toucan = {
new Toucan {
override def configNamespace = "toucan"
override def globalConfig = new Config(map)
qSettings = new QSettings
qSettings.runName = "test"
}
}
@Test
def testDefault: Unit = {
val pipeline = initPipeline(ToucanTest.config)
pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
pipeline.script()
}
@Test
def testGonl: Unit = {
val pipeline = initPipeline(ToucanTest.config ++ Map("gonl_vcf" -> ToucanTest.gonlVcfFile))
pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
pipeline.script()
}
@Test
def testExac: Unit = {
val pipeline = initPipeline(ToucanTest.config ++ Map("exac_vcf" -> ToucanTest.exacVcfFile))
pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
pipeline.script()
}
@Test
def testVarda: Unit = {
val pipeline = initPipeline(ToucanTest.config ++ Map("use_varda" -> true))
val gvcfFile = File.createTempFile("bla.", ".g.vcf")
pipeline.inputVcf = new File(ToucanTest.resourcePath("/chrQ2.vcf.gz"))
pipeline.inputGvcf = Some(gvcfFile)
pipeline.script()
}
}
object ToucanTest {
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
val outputDir = Files.createTempDir()
outputDir.deleteOnExit()
val gonlVcfFile: File = File.createTempFile("gonl.", ".vcf.gz")
gonlVcfFile.deleteOnExit()
val exacVcfFile: File = File.createTempFile("exac.", ".vcf.gz")
exacVcfFile.deleteOnExit()
val config = Map(
"reference_fasta" -> resourcePath("/fake_chrQ.fa"),
"output_dir" -> outputDir,
"gatk_jar" -> "test",
"varianteffectpredictor" -> Map(
"vep_script" -> "test",
"cache" -> true,
"dir" -> "test"
),
"varda_root" -> "test",
"varda_token" -> "test",
"bcftools" -> Map("exe" -> "test"),
"bedtools" -> Map("exe" -> "test"),
"manwe" -> Map("exe" -> "test")
)
}
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